Index: /issm/trunk/cron/configs/linux64_larour
===================================================================
--- /issm/trunk/cron/configs/linux64_larour	(revision 5067)
+++ /issm/trunk/cron/configs/linux64_larour	(revision 5068)
@@ -2,9 +2,11 @@
 ########### Configuration file for Eric Larour's nightly run on Linux ############
 
-#1: ISSM general configuration
-#-----------------------------
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
 
 #ISSM main directory (full pathto ISSM trunk)
 ISSM_DIR="/u/astrid-r1b/larour/issm/trunk/cron/trunk"
+#ISSM_DIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/issm2.2"
 
 #ISSM Architecture
@@ -17,27 +19,35 @@
 MATLAB_PATH="/usr/local/pkgs/matlab-7.6/"
 
-#2: ISSM Installation
-#--------------------
+#----------------------#
+# 2: ISSM Installation #
+#----------------------#
 
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="no"
+#ISSM_INSTALLATION can have 3 values:
+# - "checkout" the existing version of the code will be erased and
+#              the latest version will be checked out
+# - "update"   the directory won't be erased but ISSM will be updated
+#              ->skip to section 3
+# - "none"     leave ISSM as is in its directory
+#              ->skip to section 3
+ISSM_INSTALLATION="update"
 
 #SVN repository
 REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
+#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
 
 #execution path used for parallel runs
 EXECUTION_PATH="/u/astrid-r1b/larour/issm/execution"
 
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
+#-----------------------------------#
+# 3: External packages installation #
+#-----------------------------------#
 
-SKIPPACKAGESCOMPILATION="no"
+#ISSM_EXTERNALPACKAGES can have 3 values:
+# - "install" install all external packages listed below
+# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
+#             and DEVPACKAGESDIR)
+# - "none"    leave external packages as is
+#             ->skip to section 4
+ISSM_EXTERNALPACKAGES="none"
 EXTERNALPACKAGESDIR="/u/astrid-r1b/larour/issm/trunk/externalpackages"
 DEVPACKAGESDIR="/u/astrid-r1b/larour/issm/trunk/devpackages"
@@ -46,13 +56,16 @@
 EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
 
-#3: ISSM Compilation
-#-------------------
+#---------------------#
+# 4: ISSM Compilation #
+#---------------------#
 
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="no"
+#ISSM_COMPILATION can have 2 values:
+# - "yes" compile ISSM
+# - "no"  do not compile ISSM
+ISSM_COMPILATION="no"
 
-#4: Mail notification
-#--------------------
+#----------------------#
+# 5: Mail notification #
+#----------------------#
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
@@ -61,19 +74,21 @@
 
 #Sender email address
-EMAIL_ADRESS="eric.larourm@jpl.nasa.gov"
+EMAIL_ADRESS="eric.larour@jpl.nasa.gov"
 
-#5: Nightly run options
-#----------------------
+#------------------------#
+# 6: Nightly run options #
+#------------------------#
 
 #number of cpus used in ISSM installation and compilation (one is usually
 #safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=1
+NUMCPUS_INSTALL=8
 
 #number of cpus used in the nightly runs.
-NUMCPUS_RUN=14
+NUMCPUS_RUN=8
 
 #Nightly run options. The matlab routine nightlyrun.m will be called
 #as follows: nightlyrun($NROPTIONS). The options must be understandable
-#by Matlab and nightlyrun.m. Example: NROPTIONS="'parallel',0"
+#by Matlab and nightlyrun.m
+#ex: "'id',[101 102 103]"
 
 NROPTIONS=""
Index: sm/trunk/cron/configs/linux64_larour2
===================================================================
--- /issm/trunk/cron/configs/linux64_larour2	(revision 5067)
+++ 	(revision )
@@ -1,94 +1,0 @@
-#
-########### Configuration file for Mathieu Morlighem's nightly run on Linux ############
-
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#ISSM main directory (full pathto ISSM trunk)
-ISSM_DIR="/u/astrid-r1b/larour/issm/trunk/cron/trunk"
-#ISSM_DIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/issm2.2"
-
-#ISSM Architecture
-ISSM_ARCH="linux-gnu-amd64"
-
-#Operating System
-OS="linux64"
-
-#MATLAB path
-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/"
-
-#----------------------#
-# 2: ISSM Installation #
-#----------------------#
-
-#ISSM_INSTALLATION can have 3 values:
-# - "checkout" the existing version of the code will be erased and
-#              the latest version will be checked out
-# - "update"   the directory won't be erased but ISSM will be updated
-#              ->skip to section 3
-# - "none"     leave ISSM as is in its directory
-#              ->skip to section 3
-ISSM_INSTALLATION="none"
-
-#SVN repository
-REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
-#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
-
-#execution path used for parallel runs
-EXECUTION_PATH="/u/astrid-r1b/larour/issm/execution"
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#ISSM_EXTERNALPACKAGES can have 3 values:
-# - "install" install all external packages listed below
-# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
-#             and DEVPACKAGESDIR)
-# - "none"    leave external packages as is
-#             ->skip to section 4
-ISSM_EXTERNALPACKAGES="none"
-EXTERNALPACKAGESDIR="/u/astrid-r1b/larour/issm/trunk/externalpackages"
-DEVPACKAGESDIR="/u/astrid-r1b/larour/issm/trunk/devpackages"
-
-#List of external pakages to be installed
-EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
-
-#---------------------#
-# 4: ISSM Compilation #
-#---------------------#
-
-#ISSM_COMPILATION can have 2 values:
-# - "yes" compile ISSM
-# - "no"  do not compile ISSM
-ISSM_COMPILATION="no"
-
-#----------------------#
-# 5: Mail notification #
-#----------------------#
-
-#Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
-SKIPMAIL="no"
-
-#Sender email address
-EMAIL_ADRESS="eric.larour@jpl.nasa.gov"
-
-#------------------------#
-# 6: Nightly run options #
-#------------------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=8
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=1
-
-#Nightly run options. The matlab routine nightlyrun.m will be called
-#as follows: nightlyrun($NROPTIONS). The options must be understandable
-#by Matlab and nightlyrun.m
-#ex: "'id',[101 102 103]"
-
-NROPTIONS=""
Index: sm/trunk/cron/configs/linux64_local
===================================================================
--- /issm/trunk/cron/configs/linux64_local	(revision 5067)
+++ 	(revision )
@@ -1,79 +1,0 @@
-#
-########### Configuration file for a local nightly run on Linux ############
-
-#1: ISSM general configuration
-#-----------------------------
-
-#ISSM main directory (full pathto ISSM trunk)
-ISSM_DIR=$ISSM_DIR
-
-#ISSM Architecture
-ISSM_ARCH=$ISSM_ARCH
-
-#Operating System
-OS="linux64"
-
-#MATLAB path
-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/"
-
-#2: ISSM Installation
-#--------------------
-
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="yes"
-
-#SVN repository
-REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
-
-#execution path used for parallel runs
-EXECUTION_PATH=""
-
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
-
-SKIPPACKAGESCOMPILATION="yes"
-EXTERNALPACKAGESDIR=""
-DEVPACKAGESDIR=""
-
-#List of external pakages to be installed
-EXTERNALPACKAGES=""
-
-#3: ISSM Compilation
-#-------------------
-
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="yes"
-
-#4: Mail notification
-#--------------------
-
-#Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
-SKIPMAIL="yes"
-
-#Sender email address
-EMAIL_ADRESS=mathieu.morlighem@jpl.nasa.gov
-
-#5: Nightly run options
-#----------------------
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=1
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=7
-
-#Nightly run options. The matlab routine nightlyrun.m will be called
-#as follows: nightlyrun($NROPTIONS). The options must be understandable
-#by Matlab and nightlyrun.m
-
-NROPTIONS=""
Index: /issm/trunk/cron/configs/linux64_morlighem
===================================================================
--- /issm/trunk/cron/configs/linux64_morlighem	(revision 5067)
+++ /issm/trunk/cron/configs/linux64_morlighem	(revision 5068)
@@ -2,9 +2,11 @@
 ########### Configuration file for Mathieu Morlighem's nightly run on Linux ############
 
-#1: ISSM general configuration
-#-----------------------------
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
 
 #ISSM main directory (full pathto ISSM trunk)
 ISSM_DIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/trunk"
+#ISSM_DIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/issm2.2"
 
 #ISSM Architecture
@@ -17,42 +19,53 @@
 MATLAB_PATH="/usr/local/pkgs/matlab-7.6/"
 
-#2: ISSM Installation
-#--------------------
+#----------------------#
+# 2: ISSM Installation #
+#----------------------#
 
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="no"
+#ISSM_INSTALLATION can have 3 values:
+# - "checkout" the existing version of the code will be erased and
+#              the latest version will be checked out
+# - "update"   the directory won't be erased but ISSM will be updated
+#              ->skip to section 3
+# - "none"     leave ISSM as is in its directory
+#              ->skip to section 3
+ISSM_INSTALLATION="update"
 
 #SVN repository
 REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
+#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
 
 #execution path used for parallel runs
 EXECUTION_PATH="/u/wilkes-r1b/morlighe/ExecutionNightlyRun"
 
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
+#-----------------------------------#
+# 3: External packages installation #
+#-----------------------------------#
 
-SKIPPACKAGESCOMPILATION="no"
+#ISSM_EXTERNALPACKAGES can have 3 values:
+# - "install" install all external packages listed below
+# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
+#             and DEVPACKAGESDIR)
+# - "none"    leave external packages as is
+#             ->skip to section 4
+ISSM_EXTERNALPACKAGES="none"
 EXTERNALPACKAGESDIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/externalpackages"
 DEVPACKAGESDIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/devpackages"
 
 #List of external pakages to be installed
-EXTERNALPACKAGES="matlab mpich2 petsc metis triangle"
+EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
 
-#3: ISSM Compilation
-#-------------------
+#---------------------#
+# 4: ISSM Compilation #
+#---------------------#
 
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="no"
+#ISSM_COMPILATION can have 2 values:
+# - "yes" compile ISSM
+# - "no"  do not compile ISSM
+ISSM_COMPILATION="yes"
 
-#4: Mail notification
-#--------------------
+#----------------------#
+# 5: Mail notification #
+#----------------------#
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
@@ -63,17 +76,19 @@
 EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov"
 
-#5: Nightly run options
-#----------------------
+#------------------------#
+# 6: Nightly run options #
+#------------------------#
 
 #number of cpus used in ISSM installation and compilation (one is usually
 #safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=1
+NUMCPUS_INSTALL=8
 
 #number of cpus used in the nightly runs.
-NUMCPUS_RUN=6
+NUMCPUS_RUN=7
 
 #Nightly run options. The matlab routine nightlyrun.m will be called
 #as follows: nightlyrun($NROPTIONS). The options must be understandable
 #by Matlab and nightlyrun.m
+#ex: "'id',[101 102 103]"
 
 NROPTIONS=""
Index: sm/trunk/cron/configs/linux64_morlighem2
===================================================================
--- /issm/trunk/cron/configs/linux64_morlighem2	(revision 5067)
+++ 	(revision )
@@ -1,94 +1,0 @@
-#
-########### Configuration file for Mathieu Morlighem's nightly run on Linux ############
-
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#ISSM main directory (full pathto ISSM trunk)
-ISSM_DIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/trunk"
-#ISSM_DIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/issm2.2"
-
-#ISSM Architecture
-ISSM_ARCH="linux-gnu-amd64"
-
-#Operating System
-OS="linux64"
-
-#MATLAB path
-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/"
-
-#----------------------#
-# 2: ISSM Installation #
-#----------------------#
-
-#ISSM_INSTALLATION can have 3 values:
-# - "checkout" the existing version of the code will be erased and
-#              the latest version will be checked out
-# - "update"   the directory won't be erased but ISSM will be updated
-#              ->skip to section 3
-# - "none"     leave ISSM as is in its directory
-#              ->skip to section 3
-ISSM_INSTALLATION="update"
-
-#SVN repository
-REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
-#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
-
-#execution path used for parallel runs
-EXECUTION_PATH="/u/wilkes-r1b/morlighe/ExecutionNightlyRun"
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#ISSM_EXTERNALPACKAGES can have 3 values:
-# - "install" install all external packages listed below
-# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
-#             and DEVPACKAGESDIR)
-# - "none"    leave external packages as is
-#             ->skip to section 4
-ISSM_EXTERNALPACKAGES="none"
-EXTERNALPACKAGESDIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/externalpackages"
-DEVPACKAGESDIR="/u/wilkes-r1b/morlighe/svn/issm/trunk/devpackages"
-
-#List of external pakages to be installed
-EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
-
-#---------------------#
-# 4: ISSM Compilation #
-#---------------------#
-
-#ISSM_COMPILATION can have 2 values:
-# - "yes" compile ISSM
-# - "no"  do not compile ISSM
-ISSM_COMPILATION="no"
-
-#----------------------#
-# 5: Mail notification #
-#----------------------#
-
-#Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
-SKIPMAIL="no"
-
-#Sender email address
-EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov"
-
-#------------------------#
-# 6: Nightly run options #
-#------------------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=8
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=7
-
-#Nightly run options. The matlab routine nightlyrun.m will be called
-#as follows: nightlyrun($NROPTIONS). The options must be understandable
-#by Matlab and nightlyrun.m
-#ex: "'id',[101 102 103]"
-
-NROPTIONS=""
Index: /issm/trunk/cron/configs/linux64_seroussi
===================================================================
--- /issm/trunk/cron/configs/linux64_seroussi	(revision 5067)
+++ /issm/trunk/cron/configs/linux64_seroussi	(revision 5068)
@@ -2,6 +2,7 @@
 ########### Configuration file for Helene Seroussi's nightly run on Linux ############
 
-#1: ISSM general configuration
-#-----------------------------
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
 
 #ISSM main directory (full pathto ISSM trunk)
@@ -17,42 +18,53 @@
 MATLAB_PATH="/usr/local/pkgs/matlab-7.6/"
 
-#2: ISSM Installation
-#--------------------
+#----------------------#
+# 2: ISSM Installation #
+#----------------------#
 
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="no"
+#ISSM_INSTALLATION can have 3 values:
+# - "checkout" the existing version of the code will be erased and
+#              the latest version will be checked out
+# - "update"   the directory won't be erased but ISSM will be updated
+#              ->skip to section 3
+# - "none"     leave ISSM as is in its directory
+#              ->skip to section 3
+ISSM_INSTALLATION="update"
 
 #SVN repository
 REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
+#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
 
 #execution path used for parallel runs
 EXECUTION_PATH="/u/wilkes-r1b/seroussi/ExecutionNightlyRun"
 
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
+#-----------------------------------#
+# 3: External packages installation #
+#-----------------------------------#
 
-SKIPPACKAGESCOMPILATION="no"
+#ISSM_EXTERNALPACKAGES can have 3 values:
+# - "install" install all external packages listed below
+# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
+#             and DEVPACKAGESDIR)
+# - "none"    leave external packages as is
+#             ->skip to section 4
+ISSM_EXTERNALPACKAGES="none"
 EXTERNALPACKAGESDIR="/u/wilkes-r1b/seroussi/svn/issm/trunk/externalpackages"
 DEVPACKAGESDIR="/u/wilkes-r1b/seroussi/svn/issm/trunk/devpackages"
 
 #List of external pakages to be installed
-EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota"
+EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
 
-#3: ISSM Compilation
-#-------------------
+#---------------------#
+# 4: ISSM Compilation #
+#---------------------#
 
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="no"
+#ISSM_COMPILATION can have 2 values:
+# - "yes" compile ISSM
+# - "no"  do not compile ISSM
+ISSM_COMPILATION="yes"
 
-#4: Mail notification
-#--------------------
+#----------------------#
+# 5: Mail notification #
+#----------------------#
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
@@ -63,17 +75,19 @@
 EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov"
 
-#5: Nightly run options
-#----------------------
+#------------------------#
+# 6: Nightly run options #
+#------------------------#
 
 #number of cpus used in ISSM installation and compilation (one is usually
 #safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=1
+NUMCPUS_INSTALL=8
 
 #number of cpus used in the nightly runs.
-NUMCPUS_RUN=8
+NUMCPUS_RUN=7
 
 #Nightly run options. The matlab routine nightlyrun.m will be called
 #as follows: nightlyrun($NROPTIONS). The options must be understandable
 #by Matlab and nightlyrun.m
+#ex: "'id',[101 102 103]"
 
 NROPTIONS=""
Index: sm/trunk/cron/configs/macosx32_local
===================================================================
--- /issm/trunk/cron/configs/macosx32_local	(revision 5067)
+++ 	(revision )
@@ -1,79 +1,0 @@
-#
-########### Configuration file for a local nightly run on Mac ############
-
-#1: ISSM general configuration
-#-----------------------------
-
-#ISSM main directory (full pathto ISSM trunk)
-ISSM_DIR=$ISSM_DIR
-
-#ISSM Architecture
-ISSM_ARCH=$ISSM_ARCH
-
-#Operating System
-OS="macosx32"
-
-#MATLAB path
-MATLAB_PATH="/Applications/MATLAB_R2009a.app/"
-
-#2: ISSM Installation
-#--------------------
-
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="yes"
-
-#SVN repository
-REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
-
-#execution path used for parallel runs
-EXECUTION_PATH=""
-
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
-
-SKIPPACKAGESCOMPILATION="yes"
-EXTERNALPACKAGESDIR=""
-DEVPACKAGESDIR=""
-
-#List of external pakages to be installed
-EXTERNALPACKAGES=""
-
-#3: ISSM Compilation
-#-------------------
-
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="yes"
-
-#4: Mail notification
-#--------------------
-
-#Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
-SKIPMAIL="yes"
-
-#Sender email address
-EMAIL_ADRESS=mathieu.morlighem@jpl.nasa.gov
-
-#5: Nightly run options
-#----------------------
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=1
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=1
-
-#Nightly run options. The matlab routine nightlyrun.m will be called
-#as follows: nightlyrun($NROPTIONS). The options must be understandable
-#by Matlab and nightlyrun.m
-
-NROPTIONS="'parallel',0"
Index: sm/trunk/cron/configs/macosx32_morlighem
===================================================================
--- /issm/trunk/cron/configs/macosx32_morlighem	(revision 5067)
+++ 	(revision )
@@ -1,79 +1,0 @@
-#
-########### Configuration file for Mathieu Morlighem nightly run on MAC ############
-
-#1: ISSM general configuration
-#-----------------------------
-
-#ISSM main directory (full pathto ISSM trunk)
-ISSM_DIR="/Users/morlighe/Desktop/Glaciology/svn/issm/trunk/cron/trunk"
-
-#ISSM Architecture
-ISSM_ARCH="macosx-gnu"
-
-#Operating System
-OS="macosx32"
-
-#MATLAB path
-MATLAB_PATH="/Applications/MATLAB_R2009a.app/"
-
-#2: ISSM Installation
-#--------------------
-
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="no"
-
-#SVN repository
-REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
-
-#execution path used for parallel runs
-EXECUTION_PATH=""
-
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
-
-SKIPPACKAGESCOMPILATION="no"
-EXTERNALPACKAGESDIR=""
-DEVPACKAGESDIR=""
-
-#List of external pakages to be installed
-EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota"
-
-#3: ISSM Compilation
-#-------------------
-
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="no"
-
-#4: Mail notification
-#--------------------
-
-#Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
-SKIPMAIL="no"
-
-#Sender email address
-EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov"
-
-#5: Nightly run options
-#----------------------
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=1
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=2
-
-#Nightly run options. The matlab routine nightlyrun.m will be called
-#as follows: nightlyrun($NROPTIONS). The options must be understandable
-#by Matlab and nightlyrun.m
-
-NROPTIONS="'parallel',0"
Index: /issm/trunk/cron/configs/macosx32_seroussi
===================================================================
--- /issm/trunk/cron/configs/macosx32_seroussi	(revision 5067)
+++ /issm/trunk/cron/configs/macosx32_seroussi	(revision 5068)
@@ -1,7 +1,8 @@
 #
-########### Configuration file for Helene Seroussi's nightly run on MAC ############
+########### Configuration file for Helene Seroussi's nightly run on Linux ############
 
-#1: ISSM general configuration
-#-----------------------------
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
 
 #ISSM main directory (full pathto ISSM trunk)
@@ -17,42 +18,53 @@
 MATLAB_PATH="/Applications/MATLAB_R2009a.app/"
 
-#2: ISSM Installation
-#--------------------
+#----------------------#
+# 2: ISSM Installation #
+#----------------------#
 
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="no"
+#ISSM_INSTALLATION can have 3 values:
+# - "checkout" the existing version of the code will be erased and
+#              the latest version will be checked out
+# - "update"   the directory won't be erased but ISSM will be updated
+#              ->skip to section 3
+# - "none"     leave ISSM as is in its directory
+#              ->skip to section 3
+ISSM_INSTALLATION="update"
 
 #SVN repository
 REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
+#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
 
 #execution path used for parallel runs
 EXECUTION_PATH=""
 
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
+#-----------------------------------#
+# 3: External packages installation #
+#-----------------------------------#
 
-SKIPPACKAGESCOMPILATION="no"
+#ISSM_EXTERNALPACKAGES can have 3 values:
+# - "install" install all external packages listed below
+# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
+#             and DEVPACKAGESDIR)
+# - "none"    leave external packages as is
+#             ->skip to section 4
+ISSM_EXTERNALPACKAGES="none"
 EXTERNALPACKAGESDIR=""
 DEVPACKAGESDIR=""
 
 #List of external pakages to be installed
-EXTERNALPACKAGES=""
+EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
 
-#3: ISSM Compilation
-#-------------------
+#---------------------#
+# 4: ISSM Compilation #
+#---------------------#
 
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="no"
+#ISSM_COMPILATION can have 2 values:
+# - "yes" compile ISSM
+# - "no"  do not compile ISSM
+ISSM_COMPILATION="yes"
 
-#4: Mail notification
-#--------------------
+#----------------------#
+# 5: Mail notification #
+#----------------------#
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
@@ -63,6 +75,7 @@
 EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov"
 
-#5: Nightly run options
-#----------------------
+#------------------------#
+# 6: Nightly run options #
+#------------------------#
 
 #number of cpus used in ISSM installation and compilation (one is usually
@@ -76,4 +89,5 @@
 #as follows: nightlyrun($NROPTIONS). The options must be understandable
 #by Matlab and nightlyrun.m
+#ex: "'id',[101 102 103]"
 
-NROPTIONS="'parallel',0"
+NROPTIONS=""
Index: /issm/trunk/cron/configs/winxp32_larour
===================================================================
--- /issm/trunk/cron/configs/winxp32_larour	(revision 5067)
+++ /issm/trunk/cron/configs/winxp32_larour	(revision 5068)
@@ -1,7 +1,8 @@
 #
-########### Configuration file for Eric Larour's nightly run on Windows ############
+########### Configuration file for Eric Larour's nightly run on Linux ############
 
-#1: ISSM general configuration
-#-----------------------------
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
 
 #ISSM main directory (full pathto ISSM trunk)
@@ -17,42 +18,53 @@
 MATLAB_PATH="C:/MATLAB/R2009a/"
 
-#2: ISSM Installation
-#--------------------
+#----------------------#
+# 2: ISSM Installation #
+#----------------------#
 
-#ISSM installation. If SKIPINSTALLATION="no" the existing version of the 
-#code will be erased. The new version will be checked out and fully 
-#installed. If SKIPINSTALLATION="yes", the following options won't be
-#used. Go to section 3
-
-SKIPINSTALLATION="no"
+#ISSM_INSTALLATION can have 3 values:
+# - "checkout" the existing version of the code will be erased and
+#              the latest version will be checked out
+# - "update"   the directory won't be erased but ISSM will be updated
+#              ->skip to section 3
+# - "none"     leave ISSM as is in its directory
+#              ->skip to section 3
+ISSM_INSTALLATION="update"
 
 #SVN repository
 REPOSITORY="http://s383-rhat/issm/svn/issm/trunk"
+#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2"
 
 #execution path used for parallel runs
-EXECUTION_PATH=""
+EXECUTION_PATH="/u/astrid-r1b/larour/issm/execution"
 
-#External packages installation. If SKIPPACKAGESCOMPILATION="no" the
-#packages mentionned in EXTERNALPACKAGES will be fully installed which
-#requires a long time. If SKIPPACKAGESCOMPILATION="yes", the external 
-#packages directory will be removed and the directories 
-#EXTERNALPACKAGESDIR and DEVPACKAGESDIR will be copied.
+#-----------------------------------#
+# 3: External packages installation #
+#-----------------------------------#
 
-SKIPPACKAGESCOMPILATION="yes"
+#ISSM_EXTERNALPACKAGES can have 3 values:
+# - "install" install all external packages listed below
+# - "copy"    copy existing directories (EXTERNALPACKAGESDIR
+#             and DEVPACKAGESDIR)
+# - "none"    leave external packages as is
+#             ->skip to section 4
+ISSM_EXTERNALPACKAGES="none"
 EXTERNALPACKAGESDIR="/cygdrive/c/home/externalpackages"
 DEVPACKAGESDIR="/cygdrive/c/home/devpackages"
 
 #List of external pakages to be installed
-EXTERNALPACKAGES="matlab petsc metis triangle dakota"
+EXTERNALPACKAGES="matlab mpich2 petsc metis triangle dakota chaco"
 
-#3: ISSM Compilation
-#-------------------
+#---------------------#
+# 4: ISSM Compilation #
+#---------------------#
 
-#ISSM compilation. If SKIPCOMPILATION="no" ISSM will be reconfigured
-#and compiled.
-SKIPCOMPILATION="no"
+#ISSM_COMPILATION can have 2 values:
+# - "yes" compile ISSM
+# - "no"  do not compile ISSM
+ISSM_COMPILATION="no"
 
-#4: Mail notification
-#--------------------
+#----------------------#
+# 5: Mail notification #
+#----------------------#
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
@@ -63,6 +75,7 @@
 EMAIL_ADRESS="eric.larour@jpl.nasa.gov"
 
-#5: Nightly run options
-#----------------------
+#------------------------#
+# 6: Nightly run options #
+#------------------------#
 
 #number of cpus used in ISSM installation and compilation (one is usually
@@ -76,4 +89,5 @@
 #as follows: nightlyrun($NROPTIONS). The options must be understandable
 #by Matlab and nightlyrun.m
+#ex: "'id',[101 102 103]"
 
-NROPTIONS="'parallel',0"
+NROPTIONS=""
Index: /issm/trunk/cron/cronfiles/linux_cronfile
===================================================================
--- /issm/trunk/cron/cronfiles/linux_cronfile	(revision 5067)
+++ /issm/trunk/cron/cronfiles/linux_cronfile	(revision 5068)
@@ -5,5 +5,8 @@
 MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov
 
-#cronjob: issm sunday-friday 9:00pm
-30 12 * * * cd /u/astrid-r1b/larour/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_larour
-0 23 * * * cd /u/astrid-r1b/larour/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_larour
+#cronjob
+00 09 * * 1-5 cd /u/wilkes-r1b/morlighe/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_morlighem
+30 12 * * 1-5 cd /u/wilkes-r1b/morlighe/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_morlighem
+00 15 * * 1-5 cd /u/wilkes-r1b/morlighe/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_morlighem
+00 18 * * 1-5 cd /u/wilkes-r1b/morlighe/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_morlighem
+00 23 * * 1-5 cd /u/wilkes-r1b/morlighe/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/linux64_morlighem2
Index: /issm/trunk/cron/nightlyrun.sh
===================================================================
--- /issm/trunk/cron/nightlyrun.sh	(revision 5067)
+++ /issm/trunk/cron/nightlyrun.sh	(revision 5068)
@@ -78,6 +78,6 @@
 
 #Lauch installation
-#Checkout and install ISSM if requested (SKIPINSTALLATION){{{1
-if [ "$SKIPINSTALLATION" != "yes" ]
+#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{1
+if [ "$ISSM_INSTALLATION" == "checkout" ]
 then
 
@@ -86,10 +86,29 @@
 	svn checkout $REPOSITORY
 
-	#source environment variables with new matlab path
-	cd $ISSM_DIR/etc
-	source environment.sh MATLAB_DIR=$MATLAB_PATH
-
-	#create simpler  cluster.rc file, with only the cluster we are interested in.
-	cat << END > cluster.rc
+elif [ "$ISSM_INSTALLATION" == "update" ]
+then
+
+	#only update ISSM
+	cd $ISSM_DIR
+	svn update
+
+elif [ "$ISSM_INSTALLATION" == "none" ]
+then
+
+	#do nothing
+	echo "Skipping ISSM installation"
+
+else
+
+	#Error message
+	echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr.
+	exit 1
+
+fi
+#}}}
+#Create cluster.rc {{{1
+#create simpler  cluster.rc file, with only the cluster we are interested in.
+cd $ISSM_DIR/etc
+cat << END > cluster.rc
 begin
 cluster_name=$HOST_NAME
@@ -101,55 +120,66 @@
 end
 END
-
-	#Compile external packages if requested    (SKIPPACKAGESCOMPILATION){{{2
-	if [ "$SKIPPACKAGESCOMPILATION"  = "yes" ]
-	then
-
-		#erase externapackages, and link with externalpackages_dir
-		cd $ISSM_DIR
-		rm -rf externalpackages
-		cp -Rf $EXTERNALPACKAGESDIR ./
-
-		rm -rf devpackages
-		cp -Rf $DEVPACKAGESDIR ./
-	else
-		
-		cd $ISSM_DIR/externalpackages
-		for ep in $EXTERNALPACKAGES
-		do 
-			cd $ep
-			if [ "$ep" == "petsc" ]
-			then
-				#For Petsc (2.3 for now)
-				cp configs/2.3.2-p3/$OS/* . 
-				#cp configs/3.0.0-p11/$OS/* . 
-				#cat install.sh | sed -e "s/version='2.3.2-p3'/version='3.0.0-p11'/g" > temp.sh
-				#mv temp.sh install.sh
-			else
-				cp configs/$OS/* .
-			fi
-			./install.sh $NUMCPUS_INSTALL
-			cd ..
-		done
-
-		#3: install automake and autoconf
-		cd $ISSM_DIR/devpackages
-		make
+#}}}
+#Source environment variables with new matlab path {{{1
+cd $ISSM_DIR/etc
+source environment.sh MATLAB_DIR=$MATLAB_PATH
+#}}}
+#install/copy/none external packages    (ISSM_EXTERNALPACKAGES){{{1
+if [ "$ISSM_EXTERNALPACKAGES" == "install" ]
+then
+	cd $ISSM_DIR/externalpackages
+	for ep in $EXTERNALPACKAGES
+	do 
+		cd $ep
+		if [ "$ep" == "petsc" ]
+		then
+			#For Petsc (2.3 for now)
+			cp configs/2.3.2-p3/$OS/* . 
+			#cp configs/3.0.0-p11/$OS/* . 
+			#cat install.sh | sed -e "s/version='2.3.2-p3'/version='3.0.0-p11'/g" > temp.sh
+			#mv temp.sh install.sh
+		else
+			cp configs/$OS/* .
+		fi
+		./install.sh $NUMCPUS_INSTALL
 		cd ..
-	fi
-	#}}}
+	done
+
+	#3: install automake and autoconf
+	cd $ISSM_DIR/devpackages
+	make
+	cd ..
+
+elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ]
+then
+
+	#erase externapackages, and link with externalpackages_dir
+	cd $ISSM_DIR
+	rm -rf externalpackages
+	cp -Rf $EXTERNALPACKAGESDIR ./
+
+	rm -rf devpackages
+	cp -Rf $DEVPACKAGESDIR ./
+
+elif [ "$ISSM_EXTERNALPACKAGES" == "none" ]
+then
+
+	#Do nothing
+	echo "Skipping external packages installation"
+
 else
 
-	#source environment variables with new matlab path
-	cd $ISSM_DIR/etc
-	source environment.sh MATLAB_DIR=$MATLAB_PATH
-
-fi
-#}}}
-#Compile ISSM if requested              (SKIPCOMPILATION) {{{1
-if [ "$SKIPCOMPILATION" != "yes" ]
-then
+	#Error message
+	echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr.
+	exit 1
+
+fi
+#}}}
+#ISSM compilation yes/no                (ISSM_COMPILATION) {{{1
+if [ "$ISSM_COMPILATION" == "yes" ]
+then
+
 	cd $ISSM_DIR
-	svn update
+	make distclean
 	sh scripts/automakererun.sh
 	sh configs/$OS/$OS.sh.petsc2 #use petsc2 for now
@@ -168,4 +198,17 @@
 		make -j $NUMCPUS_INSTALL install
 	fi
+
+elif [ "$ISSM_COMPILATION" == "no" ]
+then
+
+	#do nothing
+	echo "Skipping ISSM compilation"
+
+else
+
+	#Error message
+	echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr.
+	exit 1
+
 fi
 #}}}
@@ -181,11 +224,11 @@
 fi
 #}}}
-#Create NightlyRun directory and nightly.log {{{1
+#Create TEMP directory and nightly.log {{{1
 #put installation elapsed time in nightly.log
 INSTALL_TIME=$(timer)
 ELAPSED_INSTALL=$(timer $START_TIME)
-rm -rf $ISSM_DIR/test/Verification/NightlyRun
-mkdir  $ISSM_DIR/test/Verification/NightlyRun
-cat << END > $ISSM_DIR/test/Verification/NightlyRun/nightly.log
+rm -rf $ISSM_DIR/TEMP
+mkdir  $ISSM_DIR/TEMP
+cat << END > $ISSM_DIR/TEMP/nightly.log
 today:     $(echo $TODAY)
 user:      $(echo $USER)
@@ -199,12 +242,12 @@
 
 #Run tests
-#Call run.sh script{{{1
+#Call run2.sh script{{{1
 cd $ISSM_DIR/cron/
-./run.sh $1
+./run2.sh $1
 #}}}
 #Complete nightly.log {{{1
 ELAPSED_RUN=$(timer $INSTALL_TIME)
 ELAPSED_TOTAL=$(timer $START_TIME)
-cat << END >>  $ISSM_DIR/test/Verification/NightlyRun/nightly.log
+cat << END >>  $ISSM_DIR/TEMP/nightly.log
 elapsed_run:   $(echo $ELAPSED_RUN)
 elapsed_total: $(echo $ELAPSED_TOTAL)
@@ -215,6 +258,6 @@
 #Build html report {{{1
 cd $ISSM_DIR/cron/
-./report.sh
-echo "html report located in $ISSM_DIR/test/Verification/NightlyRun/report.html"
+./report2.sh
+echo "html report located in $ISSM_DIR/TEMP/report.html"
 #}}}
 #send mail if requested                  (SKIPMAIL) {{{1
@@ -231,5 +274,5 @@
 			if [ "$OS" = "linux64" ]
 			then
-				cat - $ISSM_DIR/test/Verification/NightlyRun/report.html <<HERE | /usr/lib/sendmail  -oi -t
+cat - $ISSM_DIR/TEMP/report.html <<HERE | /usr/lib/sendmail  -oi -t
 From: "ISSM Nightly run" <$EMAIL_ADRESS>
 To: $i
@@ -239,5 +282,5 @@
 HERE
 		else
-cat - $ISSM_DIR/test/Verification/NightlyRun/report.html <<HERE | /usr/sbin/sendmail  -oi -t
+cat - $ISSM_DIR/TEMP/report.html <<HERE | /usr/sbin/sendmail  -oi -t
 From: "ISSM Nightly run" <$EMAIL_ADRESS>
 To: $i
Index: sm/trunk/cron/nightlyrun2.sh
===================================================================
--- /issm/trunk/cron/nightlyrun2.sh	(revision 5067)
+++ 	(revision )
@@ -1,295 +1,0 @@
-#!/bin/bash
-#This bash script calls the nightlyrun.m matlab file to run our nightly test decks. 
-#It then processes the results and sends an email to the Ice developpers.
-
-#some functions
-function timer() #{{{1
-{
-	if [[ $# -eq 0 ]]; then
-		echo $(date '+%s')
-	else
-		local  stime=$1
-		etime=$(date '+%s')
-
-		if [[ -z "$stime" ]]; then stime=$etime; fi
-
-		dt=$((etime - stime))
-		ds=$((dt % 60))
-		dm=$(((dt / 60) % 60))
-		dh=$((dt / 3600))
-		printf '%d:%02d:%02d' $dh $dm $ds
-	fi
-} #}}}
-function todaydate() #{{{1
-{
-	suffix=`date | awk '{printf("%s-%s-%s  %s",$2,$3,$6,$4);}'`			 
-	echo $suffix;			 
-} #}}}
-function host_name() #{{{1
-{
-	#return host name depending on the OS
-	if [ "$1" = "winxp32" ] 
-	then
-		HOST_NAME=`hostname`;
-	else
-		HOST_NAME=`hostname -s`;
-	fi
-	echo $HOST_NAME;
-} #}}}
-
-#Get configuration
-#Check that no other nightly run is running {{{1
-if [ "$(ps aux | grep "nighltyrun\.sh" | grep -v "grep")" ]
-then
-	echo "WARNING: A nightly run is already running. Killing..."
-
-	for JOBID in $(ps aux | grep "nighltyrun\.sh" | grep -v "grep" | awk '{printf("%s\n",$2);}');
-	do
-		kill -9 $JOBID;
-	done;
-fi
-#}}}
-#Source config file{{{1
-if [ $# -ne 1 ];
-then
-	#no config file specified: exit
-	echo "no config file specified. Exiting..." >&2 # Error message to stderr.
-	exit 1
-fi
-if [ ! -f "$1" ]
-then
-	echo "File $1 not found!" >&2   # Error message to stderr.
-	exit 1
-fi 
-source $1;
-#}}}
-#Export ISSM_* variables{{{1
-export ISSM_DIR
-export ISSM_ARCH
-#}}}
-#Initialize variables {{{1
-TODAY=$(todaydate);
-HOST_NAME=$(host_name $OS);
-START_TIME=$(timer);
-ISSM_RELEASE=$(basename $(echo $REPOSITORY));
-USER=$(whoami);
-INIT_PATH=$(pwd);
-#}}}
-
-#Lauch installation
-#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{1
-if [ "$ISSM_INSTALLATION" == "checkout" ]
-then
-
-	#Erase previous code and Fetch the new one
-	rm -rf $ISSM_RELEASE
-	svn checkout $REPOSITORY
-
-elif [ "$ISSM_INSTALLATION" == "update" ]
-then
-
-	#only update ISSM
-	cd $ISSM_DIR
-	svn update
-
-elif [ "$ISSM_INSTALLATION" == "none" ]
-then
-
-	#do nothing
-	echo "Skipping ISSM installation"
-
-else
-
-	#Error message
-	echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr.
-	exit 1
-
-fi
-#}}}
-#Create cluster.rc {{{1
-#create simpler  cluster.rc file, with only the cluster we are interested in.
-cd $ISSM_DIR/etc
-cat << END > cluster.rc
-begin
-cluster_name=$HOST_NAME
-cluster_codepath=$ISSM_DIR/bin
-cluster_executionpath=$EXECUTION_PATH
-cluster_login=$USER
-cluster_port=0
-
-end
-END
-#}}}
-#Source environment variables with new matlab path {{{1
-cd $ISSM_DIR/etc
-source environment.sh MATLAB_DIR=$MATLAB_PATH
-#}}}
-#install/copy/none external packages    (ISSM_EXTERNALPACKAGES){{{1
-if [ "$ISSM_EXTERNALPACKAGES" == "install" ]
-then
-	cd $ISSM_DIR/externalpackages
-	for ep in $EXTERNALPACKAGES
-	do 
-		cd $ep
-		if [ "$ep" == "petsc" ]
-		then
-			#For Petsc (2.3 for now)
-			cp configs/2.3.2-p3/$OS/* . 
-			#cp configs/3.0.0-p11/$OS/* . 
-			#cat install.sh | sed -e "s/version='2.3.2-p3'/version='3.0.0-p11'/g" > temp.sh
-			#mv temp.sh install.sh
-		else
-			cp configs/$OS/* .
-		fi
-		./install.sh $NUMCPUS_INSTALL
-		cd ..
-	done
-
-	#3: install automake and autoconf
-	cd $ISSM_DIR/devpackages
-	make
-	cd ..
-
-elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ]
-then
-
-	#erase externapackages, and link with externalpackages_dir
-	cd $ISSM_DIR
-	rm -rf externalpackages
-	cp -Rf $EXTERNALPACKAGESDIR ./
-
-	rm -rf devpackages
-	cp -Rf $DEVPACKAGESDIR ./
-
-elif [ "$ISSM_EXTERNALPACKAGES" == "none" ]
-then
-
-	#Do nothing
-	echo "Skipping external packages installation"
-
-else
-
-	#Error message
-	echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr.
-	exit 1
-
-fi
-#}}}
-#ISSM compilation yes/no                (ISSM_COMPILATION) {{{1
-if [ "$ISSM_COMPILATION" == "yes" ]
-then
-
-	cd $ISSM_DIR
-	make distclean
-	sh scripts/automakererun.sh
-	sh configs/$OS/$OS.sh.petsc2 #use petsc2 for now
-	#sh configs/$OS/$OS.sh.petsc3 #switch to petsc3 to debug
-
-	#4: compile and install ISSM
-	if [ "$OS" = "winxp32" ] 
-	then
-		cd $ISSM_DIR/src/c
-		./intel-compile.sh
-		cd $ISSM_DIR/src/mex
-		make install
-		cd $ISSM_DIR
-	else
-		make -j $NUMCPUS_INSTALL
-		make -j $NUMCPUS_INSTALL install
-	fi
-
-elif [ "$ISSM_COMPILATION" == "no" ]
-then
-
-	#do nothing
-	echo "Skipping ISSM compilation"
-
-else
-
-	#Error message
-	echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr.
-	exit 1
-
-fi
-#}}}
-
-#Prepare run
-#Windows hack for startup.m {{{1
-#windows environments: ISSM_DIR_WIN variable not correctly picked up when using 
-#the cron job. just get startup to take the ISSM_DIR variable as the pwd:
-if [ "$OS" = "winxp32" ]
-then
-	cat startup.m | sed 's/clear status/clear status; ISSM_DIR=pwd;/g' > startup.m.bak
-	mv startup.m.bak startup.m
-fi
-#}}}
-#Create TEMP directory and nightly.log {{{1
-#put installation elapsed time in nightly.log
-INSTALL_TIME=$(timer)
-ELAPSED_INSTALL=$(timer $START_TIME)
-rm -rf $ISSM_DIR/TEMP
-mkdir  $ISSM_DIR/TEMP
-cat << END > $ISSM_DIR/TEMP/nightly.log
-today:     $(echo $TODAY)
-user:      $(echo $USER)
-host:      $(echo $HOST_NAME)
-OS:        $(echo $OS)
-release:   $(echo $ISSM_RELEASE)
-init_path: $(echo $INIT_PATH)
-elapsed_install: $(echo $ELAPSED_INSTALL)
-END
-#}}}
-
-#Run tests
-#Call run2.sh script{{{1
-cd $ISSM_DIR/cron/
-./run2.sh $1
-#}}}
-#Complete nightly.log {{{1
-ELAPSED_RUN=$(timer $INSTALL_TIME)
-ELAPSED_TOTAL=$(timer $START_TIME)
-cat << END >>  $ISSM_DIR/TEMP/nightly.log
-elapsed_run:   $(echo $ELAPSED_RUN)
-elapsed_total: $(echo $ELAPSED_TOTAL)
-END
-#}}}
-
-#Send Report
-#Build html report {{{1
-cd $ISSM_DIR/cron/
-./report2.sh
-echo "html report located in $ISSM_DIR/TEMP/report.html"
-#}}}
-#send mail if requested                  (SKIPMAIL) {{{1
-if [ "$SKIPMAIL" != "yes" ]
-then
-	echo "sending report..."
-	source $ISSM_DIR/cron/mailinglist
-	for i in `echo $MAILINGLIST`; do
-
-		if [ "$OS" = "winxp32" ]
-		then
-			email -html -f "ISSM Nightly run $EMAIL_ADRESS" -s "Nightly runs of $ISSM_RELEASE , operating system: $OS, host: $HOST_NAME, user: $USER. " $i < $ISSM_DIR/test/Verification/NightlyRun/report.html
-		else 
-			if [ "$OS" = "linux64" ]
-			then
-cat - $ISSM_DIR/TEMP/report.html <<HERE | /usr/lib/sendmail  -oi -t
-From: "ISSM Nightly run" <$EMAIL_ADRESS>
-To: $i
-Subject: Nightly runs of $ISSM_RELEASE, operating system: $OS, host: $HOST_NAME, user: $USER.
-Mime-Version: 1.0
-Content-Type: text/html
-HERE
-		else
-cat - $ISSM_DIR/TEMP/report.html <<HERE | /usr/sbin/sendmail  -oi -t
-From: "ISSM Nightly run" <$EMAIL_ADRESS>
-To: $i
-Subject: Nightly runs of $ISSM_RELEASE, operating system: $OS, host: $HOST_NAME, user: $USER.
-Mime-Version: 1.0
-Content-Type: text/html
-HERE
-			fi
-		fi
-	done
-fi
-#}}}
Index: /issm/trunk/cron/report.sh
===================================================================
--- /issm/trunk/cron/report.sh	(revision 5067)
+++ /issm/trunk/cron/report.sh	(revision 5068)
@@ -3,5 +3,5 @@
 
 #First go to the nightly run directory (created by nightlyrun.sh)
-cd $ISSM_DIR/test/Verification/NightlyRun/
+cd $ISSM_DIR/nightlylog/
 
 #----------------------------#
@@ -39,6 +39,6 @@
 MATLAB_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px; font-weight: normal;" align="left"'
 
-BODY_STYLE='width="1050px"'
-BODY_FONT="style=\"color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px;\""
+BODY_STYLE='width="800px"'
+BODY_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px;"'
 
 FOOTER_STYLE='width="800px"  cellpadding="10"'
@@ -128,11 +128,6 @@
 <th $(echo $BODY_FONT)>Result</th> 
 <th $(echo $BODY_FONT)>Tolerance</th> 
-<th $(echo $BODY_FONT)>Test name</th>  
-<th $(echo $BODY_FONT)>Analysis</th> 
-<th $(echo $BODY_FONT)>Subanalysis </th> 
-<th $(echo $BODY_FONT)>Qmu</th>
-<th $(echo $BODY_FONT)>Control</th>
-<th $(echo $BODY_FONT)>Control fit</th>
-<th $(echo $BODY_FONT)>Parallel</th>
+<th $(echo $BODY_FONT)>Test id</th>  
+<th $(echo $BODY_FONT)>Test name</th> 
 <th $(echo $BODY_FONT)>Field checked</th>
 </tr>
@@ -151,5 +146,5 @@
 		  FONTL=$(echo "$BODY_FONTL bgcolor=#ffff00");
 		  echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" '
-		  { printf("<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n",FONTL,$1,FONTC,"N/A",FONTL,$3,FONTL,$5,FONTL,$7,FONTC,$9,FONTC,$11,FONTC,$13,FONTC,$15,FONTC,"N/A");}
+		  { printf("<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n\n",FONTL,$1,FONTC,$3,FONTC,$6,FONTL,$9,FONTL,$11);}
 			  '; 
 
@@ -169,5 +164,5 @@
 		  FONTL=$(echo "$BODY_FONTL $color")
 		  echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" '
-		  { printf("<td %s>%s</td>\n<td %s>%s%s%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n",FONTL,$1,FONTL,$3,$4,$5,FONTL,$7,FONTL,$9,FONTL,$11,FONTC,$13,FONTC,$15,FONTC,$17,FONTC,$19,FONTL,$21);}
+		  { printf("<td %s>%s</td>\n<td %s>%s%s%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n\n",FONTL,$1,FONTL,$3,$4,$5,FONTC,$8,FONTL,$11,FONTL,$13);}
 			  '; 
 	  fi
Index: sm/trunk/cron/report2.sh
===================================================================
--- /issm/trunk/cron/report2.sh	(revision 5067)
+++ 	(revision )
@@ -1,203 +1,0 @@
-#!/bin/bash
-#generate html report from nightly.log output file
-
-#First go to the nightly run directory (created by nightlyrun.sh)
-cd $ISSM_DIR/TEMP/
-
-#----------------------------#
-# Initialize local variables #
-#----------------------------#
-
-#process nightly.log
-TODAY=`     cat nightly.log | grep "today"           | awk '{printf("%s %s",$2,$3);}'`
-USER=`      cat nightly.log | grep "user"            | awk '{print $2}'`
-HOST_NAME=` cat nightly.log | grep "host"            | awk '{print $2}'`
-OS=`        cat nightly.log | grep "OS"              | awk '{print $2}'`
-RELEASE=`   cat nightly.log | grep "release"         | awk '{print $2}'`
-EL_INSTALL=`cat nightly.log | grep "elapsed_install" | awk '{print $2}'`
-EL_RUN=`    cat nightly.log | grep "elapsed_run"     | awk '{print $2}'`
-EL_TOTAL=`  cat nightly.log | grep "elapsed_total"   | awk '{print $2}'`
-
-#Process matlab_log.log
-cat matlab_log.log        | egrep 'ERROR|SUCCESS|FAILURE' | sed -e "s/>/\&gt;/g" | sed -e "s/</\&lt;/g" > matlab.log
-NUM_TOT=`wc -l matlab.log | awk '{print $1}'`
-NUM_ERR=`cat matlab.log | grep 'ERROR'   | grep -v "PETSC ERROR" | wc -l`
-NUM_SUC=`cat matlab.log | grep 'SUCCESS' | wc -l`
-NUM_FAI=`cat matlab.log | grep 'FAILURE' | wc -l`
-
-#style
-H1_STYLE='width="1000px" cellpadding="20"'
-H1_FONT='style="color:#6495ed; font-family:Arial, Verdana, Tahoma; font-weight: bold; font-size:35px;" align="center"'
-
-H2_STYLE='width="900px" cellpadding="20"'
-H2_FONT='style="color:#6495ed; font-family:Arial, Verdana, Tahoma; font-size:28px; font-weight: bold;" align="left"'
-
-TABLE_STYLE='width="800px" rules=none bgcolor="#ffffdd" border=1 bordercolor="#000000" cellpadding="3"'
-TABLE_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14; font-weight: normal;" align="left"'
-
-MATLAB_STYLE='width="1000px" rules=none'
-MATLAB_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px; font-weight: normal;" align="left"'
-
-BODY_STYLE='width="800px"'
-BODY_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:14px;"'
-
-FOOTER_STYLE='width="800px"  cellpadding="10"'
-FOOTER_FONT='style="color:#404040; font-family:Arial, Verdana, Tahoma; font-size:12px; font-weight: normal;" align="center"'
-
-#style 2
-BODY_FONTC=`echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:center; /g"`
-BODY_FONTL=`echo $BODY_FONT | sed -e "s/style=\"/style=\"text-align:left; /g"`
-
-#create some variables
-if [ $(ls -1 $ISSM_DIR/bin | wc -l) -le 20 ];
-then
-	IS_INSTALL=0
-else
-	IS_INSTALL=1
-fi
-if [ $(wc -l matlab.log | awk '{printf("%s",$1);}')  -eq 0 ] 
-then
-	IS_RUN=0
-else
-	IS_RUN=1
-fi
-
-#-------------------#
-# build report.html #
-#-------------------#
-
-#first: summary
-cat << END > summary.html
-<div align="center">
-<table $H1_STYLE><tr><td $H1_FONT>ISSM Nightly run report</td></tr></table>
-
-<table $TABLE_STYLE>
-<tr> 
-<td $TABLE_FONT>host: $HOST_NAME</td>
-<td $TABLE_FONT>date: $TODAY</td>
-</tr>
-<tr>
-<td $TABLE_FONT>OS: $OS</td>
-<td $TABLE_FONT>user: $USER</td>
-</tr>
-<tr>
-<td $TABLE_FONT>status: STATUS</td>
-<td $TABLE_FONT>release: $RELEASE</td>
-</tr>
-<tr>
-<td $TABLE_FONT>number of success: $NUM_SUC/$NUM_TOT
-<td $TABLE_FONT>total elapsed time: $EL_TOTAL</td>
-</tr>
-<tr>
-<td $TABLE_FONT>number of errors: $NUM_ERR/$NUM_TOT
-
-<td $TABLE_FONT>installation elapsed time: $EL_INSTALL</td>
-</tr>
-<tr>
-<td $TABLE_FONT>number of failures: $NUM_FAI/$NUM_TOT
-<td $TABLE_FONT>execution elapsed time: $EL_RUN</td>
-</tr>
-</table>
-<br><hr width="1000px">
-END
-
-#update status
-if [ $IS_RUN -eq 1 ]
-then
-	cat summary.html | sed -e "s/STATUS/<span style=\"color:#008000\">all test desks have been run<\/span>/g" > summary2.html
-	mv summary2.html summary.html
-else
-	if [ $IS_INSTALL -eq 1 ]
-	then
-		cat summary.html | sed -e "s/STATUS/<span style=\"color:#ff0000\">installation successful but tests runs failed<\/span>/g" > summary2.html
-		mv summary2.html summary.html
-	else
-		cat summary.html | sed -e "s/STATUS/<span style=\"color:#ff0000\">installation failed<\/span>/g" > summary2.html
-		mv summary2.html summary.html
-	fi
-fi
-
-
-#report table
-if [ $IS_RUN -eq 1 ];
-then
-	cat << END > content.html
-<table $(echo $H2_STYLE)><tr><td $(echo $H2_FONT)>List of tests</td></tr></table>
-<table $(echo $BODY_STYLE) style="border-collapse:collapse;">
-<tr> 
-<th $(echo $BODY_FONT)>Result</th> 
-<th $(echo $BODY_FONT)>Tolerance</th> 
-<th $(echo $BODY_FONT)>Test id</th>  
-<th $(echo $BODY_FONT)>Test name</th> 
-<th $(echo $BODY_FONT)>Field checked</th>
-</tr>
-$(cat matlab.log | while read line
-  do
-	  echo "<tr>"
-
-	  #get status
-	  STATUS=`echo $line | awk '{print $1}'`
-
-	  #FAILURE
-	  if [ "$STATUS" = "FAILURE" ]
-	  then
-
-		  FONTC=$(echo "$BODY_FONTC bgcolor=#ffff00");
-		  FONTL=$(echo "$BODY_FONTL bgcolor=#ffff00");
-		  echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" '
-		  { printf("<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n\n",FONTL,$1,FONTC,$3,FONTC,$6,FONTL,$9,FONTL,$11);}
-			  '; 
-
-		  else
-
-		  #SUCCESS
-		  if [ "$STATUS" = "SUCCESS" ]
-		  then
-			  color="bgcolor=#ddffdd";
-
-		  #ERROR
-		  else
-			  color="bgcolor=#ffdddd";
-		  fi
-
-		  FONTC=$(echo "$BODY_FONTC $color")
-		  FONTL=$(echo "$BODY_FONTL $color")
-		  echo $line | awk -v FONTC="$FONTC" -v FONTL="$FONTL" '
-		  { printf("<td %s>%s</td>\n<td %s>%s%s%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n<td %s>%s</td>\n\n",FONTL,$1,FONTL,$3,$4,$5,FONTC,$8,FONTL,$11,FONTL,$13);}
-			  '; 
-	  fi
-
-	  echo "</tr>"
-
-  done
-	  )
-</table>
-<br>
-END
-else
-	mktemp content.html
-fi
-
-#Matlab error report
-if [ -e matlaberror.log ]
-then
-	cat << END > matlaberror.html
-<table $H2_STYLE><tr><td $H2_FONT>Matlab error</td></tr></table>
-<table $MATLAB_STYLE><tr><td $MATLAB_FONT>
-<pre>$(cat matlaberror.log)</pre>
-</td></tr></table>
-END
-else
-	mktemp matlaberror.html
-fi
-
-#last footer
-cat << END > footer.html
-<br>
-<table $FOOTER_STYLE><tr><td $FOOTER_FONT><a href="http://issm.jpl.nasa.gov" title="ISSM website" target="_blank">ISSM</a> nightly run report</td></tr></table>
-</div>
-END
-
-#concatenate files
-cat summary.html content.html matlaberror.html footer.html > report.html
-rm  summary.html content.html footer.html matlaberror.html matlab.log
Index: /issm/trunk/cron/run.sh
===================================================================
--- /issm/trunk/cron/run.sh	(revision 5067)
+++ /issm/trunk/cron/run.sh	(revision 5068)
@@ -1,5 +1,6 @@
 #!/bin/bash
 
-#get configs
+#prepare runs
+#get configs {{{1
 if [ $# -ne 1 ];
 then
@@ -8,9 +9,11 @@
 	exit 1
 fi
-INIT_PATH=`cat $ISSM_DIR/test/Verification/NightlyRun/nightly.log | grep "init_path" | awk '{print $2}'`
+
+#Go to init_Path and source config
+INIT_PATH=$(cat $ISSM_DIR/nightlylog/nightly.log | grep "init_path" | awk '{print $2}')
 cd $INIT_PATH
 source $1;
-
-#check NUMCPUS_RUN options
+#}}}
+#check NUMCPUS_RUN options {{{1
 if [ "$NUMCPUS_RUN" = "" ]
 then
@@ -18,8 +21,9 @@
 	NUMCPUS_RUN=1
 fi
-
-#create softlink to startup
-cd $ISSM_DIR/test/Verification/NightlyRun/
+#}}}
+#create softlink to startup {{{1
+cd $ISSM_DIR/test/NightlyRun/
 ln -s $ISSM_DIR/startup.m .
+#}}}
 
 #Launch all tests on different cpus
@@ -27,19 +31,21 @@
 do
 	#Launch matlab and the nightly run script
-	cat > $ISSM_DIR/test/Verification/NightlyRun/matlab_run$i.m << EOF
-	warning off %necessary to avoid a nightly.log of several Go for cielo_parallel
+	cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF
+	warning off %necessary to avoid a nightly.log of several Go for parallel runs
 	try,
-	$(if [ "$NROPTIONS" = ""  ]
+		cd $ISSM_DIR/test/NightlyRun
+		startup;
+		$(if [ "$NROPTIONS" = ""  ]
 	then
-		echo "nightlyrun('rank',$i,'numprocs',$NUMCPUS_RUN);"
+		echo "runme('rank',$i,'numprocs',$NUMCPUS_RUN);"
 	else
-		echo "nightlyrun($NROPTIONS,'rank',$i,'numprocs',$NUMCPUS_RUN);"
+		echo "runme($NROPTIONS,'rank',$i,'numprocs',$NUMCPUS_RUN);"
 	fi
-		)
+	)
 	catch me,
 		%An error occured, get report and exit
 		directory=strsplit(pwd,'/');
 		message=getReport(me)
-		fid=fopen([ISSM_DIR '/test/Verification/NightlyRun/matlaberror.log'], 'at');
+		fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at');
 		fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
 		fprintf(fid,'%s',message);
@@ -48,12 +54,16 @@
 	exit
 EOF
-MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8
-/usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab  -nojvm -nosplash  -r matlab_run$i -logfile matlab_log$i.log &
+
+	#Start run from nightlylog directory
+	cd $ISSM_DIR/nightlylog/
+
+	#Start test
+	MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8
+	/usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab  -nojvm -nosplash  -r matlab_run$i -logfile matlab_log$i.log &
+
 done
 
+#wait until matlab closes
 wait
-
-#remove matlab_run scripts.
-rm -rf matlab_run*.m
 
 #concatenate all reports
Index: sm/trunk/cron/run2.sh
===================================================================
--- /issm/trunk/cron/run2.sh	(revision 5067)
+++ 	(revision )
@@ -1,77 +1,0 @@
-#!/bin/bash
-
-#prepare runs
-#get configs {{{1
-if [ $# -ne 1 ];
-then
-	#no config file specified: exit
-	echo "no config file specified. Exiting..."
-	exit 1
-fi
-
-#Go to init_Path and source config
-INIT_PATH=$(cat $ISSM_DIR/TEMP/nightly.log | grep "init_path" | awk '{print $2}')
-cd $INIT_PATH
-source $1;
-#}}}
-#check NUMCPUS_RUN options {{{1
-if [ "$NUMCPUS_RUN" = "" ]
-then
-	echo "NUMCPUS_RUN option not found, defaulting to NUMCPUS_RUN = 1"
-	NUMCPUS_RUN=1
-fi
-#}}}
-#create softlink to startup {{{1
-cd $ISSM_DIR/test/NightlyRun/
-ln -s $ISSM_DIR/startup.m .
-#}}}
-
-#Launch all tests on different cpus
-for (( i=1;i<=$NUMCPUS_RUN;i++ ))
-do
-	#Launch matlab and the nightly run script
-	cat > $ISSM_DIR/TEMP/matlab_run$i.m << EOF
-	warning off %necessary to avoid a nightly.log of several Go for parallel runs
-	try,
-		cd $ISSM_DIR/test/NightlyRun
-		startup;
-		$(if [ "$NROPTIONS" = ""  ]
-	then
-		echo "runme('rank',$i,'numprocs',$NUMCPUS_RUN);"
-	else
-		echo "runme($NROPTIONS,'rank',$i,'numprocs',$NUMCPUS_RUN);"
-	fi
-	)
-	catch me,
-		%An error occured, get report and exit
-		directory=strsplit(pwd,'/');
-		message=getReport(me)
-		fid=fopen([ISSM_DIR '/TEMP/matlaberror.log'], 'at');
-		fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
-		fprintf(fid,'%s',message);
-		fclose(fid);
-	end
-	exit
-EOF
-
-	#Start run from TEMP directory
-	cd $ISSM_DIR/TEMP/
-
-	#Start test
-	MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8
-	/usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab  -nojvm -nosplash  -r matlab_run$i -logfile matlab_log$i.log &
-
-done
-
-#wait until matlab closes
-wait
-
-#concatenate all reports
-mv matlab_log1.log  matlab_log.log
-for (( i=2;i<=$NUMCPUS_RUN;i++ ))
-do
-	cat matlab_log.log matlab_log$i.log > matlab_log.log.bak
-	mv matlab_log.log.bak matlab_log.log
-	rm matlab_log$i.log
-
-done